Full-length Genome of the Ogataea polymorpha strain HU-11 reveals large duplicated segments in subtelomeric regions

Abstract Background: Currently, methylotrophic yeasts (e.g., Pichia pastoris, Hansenula polymorpha, and Candida boindii) are subjects of intense genomics studies in basic research and industrial applications. In the genus Ogataea, most research is focused on three basic O. polymorpha strains—CBS4732, NCYC495, and DL-1. However, these three strains are of independent origin and unclear relationship. As a high-yield engineered O. polymorpha strain, HU-11 can be regarded as identical to CBS4732, because the only difference between them is a 5-bp insertion. Results: In the present study, we have assembled the full-length genome of O. polymorpha HU-11 using high-depth PacBio and Illumina data. Long terminal repeat (LTR) retrotransposons, rDNA, 5' and 3' telomeric, subtelomeric, low complexity and other repeat regions were curated to improve the genome quality. We took advantage of the full-length HU-11 genome sequence for the genome annotation and comparison. Particularly, we determined the exact location of the rDNA genes and LTR retrotransposons in seven chromosomes and detected large duplicated segments in the subtelomeric regions. Three novel findings are: (1) O. polymorpha NCYC495 is so phylogenetically close to CBS4732/HU-11 that the syntenic regions covers nearly 100% of their genomes with a nucleotide identity of 99.5%, while NCYC495 is significantly distinct from DL-1; (2) large segment duplication in subtelomeric regions is the main reason for genome expansion in yeasts; and (3) the duplicated segments in subtelomeric regions may be integrated at telomeric tandem repeats (TRs) through a molecular mechanism, which can be used to develop a simple and highly efficient genome editing system to integrate or cleave large segments into yeast genomes. Conclusions: Our findings provide new opportunities for in-depth understanding of genome evolution in methylotrophic yeasts and lay the foundations for the industrial applications of O. polymorpha HU-11 and CBS4732. The full-length genome of the O. polymorpha strain HU-11 should be included into the NCBI RefSeq database for future studies of O. polymorpha CBS4732, NCYC495, and their derivative strains.

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Full-length Genome of the Ogataea polymorpha strain HU-11 reveals large duplicated segments in subtelomeic regions

10.1101/2021.04.17.440260 ◽

2021 ◽

Author(s):

Jia Chang ◽

Jinlong Bei ◽

Hemu Wang ◽

Xin Li ◽

Tung On Yau ◽

...

Keyword(s):

Tandem Repeats ◽

Hansenula Polymorpha ◽

Basic Research ◽

Low Complexity ◽

Industrial Applications ◽

Full Length ◽

High Yield ◽

Ltr Retrotransposons ◽

Methylotrophic Yeasts ◽

Full Length Genome

Background: Currently, methylotrophic yeasts (e.g., Pichia pastoris, Hansenula polymorpha, and Candida boindii) are subjects of intense genomics studies in basic research and industrial applications. In the genus Ogataea, most research is focused on three basic O. polymorpha strains—CBS4732, NCYC495, and DL-1. However, these three strains are of independent origin and unclear relationship. As a high-yield engineered O. polymorpha strain, HU-11 can be regarded as identical to CBS4732, because the only difference between them is a 5-bp insertion. Results: In the present study, we have assembled the full-length genome of O. polymorpha HU-11 using high-depth PacBio and Illumina data. Long terminal repeat (LTR) retrotransposons, rDNA, 5' and 3' telomeric, subtelomeric, low complexity and other repeat regions were curated to improve the genome quality. We took advantage of the full-length HU-11 genome sequence for the genome annotation and comparison. Particularly, we determined the exact location of the rDNA genes and LTR retrotransposons in seven chromosomes and detected large duplicated segments in the subtelomeic regions. Three novel findings are: (1) the O. polymorpha NCYC495 is so phylogenetically similar to HU11 that a nearly 100% of their genomes is covered by their syntenic regions, while NCYC495 is significantly distinct from DL-1; (2) large segment duplication in subtelomeic regions is the main reason for genome expansion in yeasts; and (3) the duplicated segments in subtelomeric regions may be integrated at telomeric tandem repeats (TRs) through a molecular mechanism, which can be used to develop a simple and highly efficient genome editing system to integrate or cleave large segments at telomeric TRs. Conclusions: Our findings provide new opportunities for in-depth understanding of genome evolution in methylotrophic yeasts and lay the foundations for the industrial applications of O. polymorpha CBS4732 and HU11. The full-length genome of the O. polymorpha strain HU-11 should be included into the NCBI RefSeq database for future studies of O. polymorpha CBS4732 and its derivatives LR9, RB11 and HU-11.

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Molecular Sieves: From Basic Research to Industrial Applications, Proceedings of the 3rd International Zeolite Symposium (3rd FEZA)

10.1016/s0167-2991(05)x8435-x ◽

2005 ◽

Keyword(s):

Molecular Sieves ◽

Basic Research ◽

Industrial Applications

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Promising Immobilization of Industrial-Class Phospholipase A1 to Attain High-Yield Phospholipids Hydrolysis and Repeated Use with Optimal Water Content in Water-in-Oil Microemulsion Phase

Applied Sciences ◽

10.3390/app11041456 ◽

2021 ◽

Vol 11 (4) ◽

pp. 1456

Author(s):

Yusuke Hayakawa ◽

Ryoichi Nakayama ◽

Norikazu Namiki ◽

Masanao Imai

Keyword(s):

Water Content ◽

Reaction Rate ◽

Enzyme Reaction ◽

Initial Reaction Rate ◽

Industrial Applications ◽

Molar Ratio ◽

High Yield ◽

Initial Reaction ◽

Phospholipase A1 ◽

Repeated Use

In this study, we maximized the reactivity of phospholipids hydrolysis with immobilized industrial-class phospholipase A1 (PLA1) at the desired water content in the water-in-oil (W/O) microemulsion phase. The optimal hydrophobic-hydrophilic condition of the reaction media in a hydrophobic enzyme reaction is critical to realize the maximum yields of enzyme activity of phospholipase A1. It was attributed to enzymes disliking hydrophobic surroundings as a special molecular structure for reactivity. Immobilization of PLA1 was successfully achieved with the aid of a hydrophobic carrier (Accurel MP100) combination with the treatment using glutaraldehyde. The immobilized yield was over 90% based on simple adsorption. The hydrolysis reaction was kinetically investigated through the effect of glutaraldehyde treatment of carrier and water content in the W/O microemulsion phase. The initial reaction rate increased linearly with an increasing glutaraldehyde concentration and then leveled off over a 6% glutaraldehyde concentration. The initial reaction rate, which was predominantly driven by the water content in the organic phase, changed according to a typical bell-shaped curve with respect to the molar ratio of water to phospholipid. It behaved in a similar way with different glutaraldehyde concentrations. After 10 cycles of repeated use, the reactivity was well sustained at 40% of the initial reaction rate and the creation of the final product. Accumulated yield after 10 times repetition was sufficient for industrial applications. Immobilized PLA1 has demonstrated potential as a biocatalyst for the production of phospholipid biochemicals.

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Full-length genome characterization of a novel alphapartitivirus detected in the ectomycorrhizal fungus Hygrophorus penarioides

Virus Genes ◽

10.1007/s11262-020-01814-9 ◽

2021 ◽

Author(s):

Ergin Sahin ◽

Ilgaz Akata

Keyword(s):

Ectomycorrhizal Fungus ◽

Full Length ◽

Genome Characterization ◽

Full Length Genome

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Next Generation Sequencing of Near-Full Length Genome of Norovirus GII.4 from Botswana

Virus Research ◽

10.1016/j.virusres.2021.198491 ◽

2021 ◽

pp. 198491

Author(s):

Kgomotso Makhaola ◽

Sikhulile Moyo ◽

Lemme P. Kebaabetswe

Keyword(s):

Next Generation Sequencing ◽

Full Length ◽

Next Generation ◽

Norovirus Gii ◽

Full Length Genome ◽

Generation Sequencing

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Emergence of Salmonid Alphavirus Genotype 2 in Norway—Molecular Characterization of Viral Strains Circulating in Norway and Scotland

Viruses ◽

10.3390/v13081556 ◽

2021 ◽

Vol 13 (8) ◽

pp. 1556

Author(s):

Monika J. Hjortaas ◽

Elena Fringuelli ◽

Adérito L. Monjane ◽

Aase B. Mikalsen ◽

Christine M. Jonassen ◽

...

Keyword(s):

Full Length ◽

Genomic Diversity ◽

Last Common Ancestor ◽

Source Of Infection ◽

New Variant ◽

Genotype 2 ◽

Boat Traffic ◽

Horizontal Spread ◽

Full Length Genome

Pancreas disease (PD) and sleeping disease (SD), caused by an alphavirus, are endemic in European salmonid aquaculture, causing significant mortality, reduced growth and poor flesh quality. In 2010, a new variant of salmonid alphavirus emerged in Norway, marine salmonid alphavirus genotype 2 (SAV2). As this genotype is highly prevalent in Scotland, transmission through well boat traffic was hypothesized as one possible source of infection. In this study, we performed full-length genome sequencing of SAV2 sampled between 2006 and 2012 in Norway and Scotland, and present the first comprehensive full-length characterization of Norwegian marine SAV2 strains. We analyze their relationship with selected Scottish SAV2 strains and explore the genetic diversity of SAV. Our results show that all Norwegian marine SAV2 share a recent last common ancestor with marine SAV2 circulating in Scotland and a higher level of genomic diversity among the Scottish marine SAV2 strains compared to strains from Norway. These findings support the hypothesis of a single introduction of SAV2 to Norway sometime from 2006–2010, followed by horizontal spread along the coast.

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